Rapid quantification of short-chain fatty acids by Fourier-transform infrared spectroscopy for microbiota quality assessment

Short-chain fatty acids (SCFAs) are bacterial metabolites with crucial roles in host homeostasis and immune system modulation. Given their benefits, they have been proposed as markers of a healthy microbiota. Their quantification, however, is time-consuming, expensive and requires specialized personal and equipment. Thus, their use for quality assessment of stool samples in clinical contexts is limited. In this study we explored the use of Fourier-transform infrared (FT-IR) spectroscopy as an alternative method for metabolomic quality assessment of stool samples. FT-IR identifies the chemical bonds present in SCFAs and allows clear discrimination between healthy and dysbiotic stool samples (caused by Clostridioides difficile infection) through Principal Component Analysis (PCA). Overall, FT-IR provides a rapid, cost-effective and simple method for stool samples quality assessment. Combined with the widespread availability of this technology in most hospitals, these advantages highlight its potential application for routine implementation in clinical laboratories.